We re-imputed our 48,943 discovery samples across the HLA (chr6:29,607,078-33,267,103 (b37)) using IMPUTE2 v2.3.1 with a reference panel incorporating classical HLA alleles and amino acid changes55. The reference panel contained haplotypes for 5,225 samples from the type 1 diabetes genetics consortium (T1DGC) across 8,961 biallelic variants comprised of 5,863 directly genotyped biallelic SNPs and 3,098 surrogate biallelic variants encoding multiallelic SNPs, indels, classical HLA alleles and amino acid changes. Association testing was then undertaken as described for stage 1 for FEV1 and FEV1/FVC.
